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Why Case Western Reserve University?

Why Case Western Reserve University?

Why Case Western Reserve School of Medicine?

Case Western Reserve University provides a unique environment for students who would like to pursue a graduate degree in Systems Biology and Bioinformatics. Ranked among the top 20 medical schools nationally, Case Western Reserve School of Medicine hosts internationally renowned faculty with cutting edge research on medical sciences.

We are the top ranked institution in the United States on the inaugural University Global Health Impact Report Card. The report card is a project of Universities Allied for Essential Medicines (UAEM), a worldwide student organization that aims to encourage institutions of higher education to improve access to the results of research - in particular, innovations in drug development and health technologies. The initiative grew out of a successful 2001 campaign by Yale law students to persuade their university and Bristol-Myers Squibb to pledge to allow generic production of an AIDS drug in sub-Saharan Africa.

For students at the Systems Biology and Bioinformatics program, the wealth of medical and translational research activities on campus offer a unique opportunity to make an impact human health. The students also greatly benefit from the collaborative atmosphere at the university, within the Case Western Reserve School of Medicine and at the Center for Proteomics and Bioinformatics. In this respect, the students are encouraged to adopt two advisors with disparate, yet related research interests.

Joint Publications Among SYBB Trainers

  1. Li, J., Zhou, Y., Elston, R.C. Haplotype-based quantitative trait mapping using a clustering algorithm BMC Bioinformatics. 2006 May 18;7:258 PMCID: PMC1533867
  2. Ramirez de Knott, H.M., McCormick, T.S., Kalka, K., Skandamis, G., Ghannoum, M.A., Schluchter, M., Cooper, K.D., Nedorost, S.T. Cutaneous hypersensitivity to Malassezia sympodialis and dust mite in adult atopic dermatitis with a textile pattern Contact Dermatitis. 2006 Feb;54(2):92-9
  3. Miller, J.D., Baron, E.D., Scull, H., Hsia, A., Berlin, J.C., McCormick, T., Colussi, V., Kenney, M.E., Cooper, K.D., Oleinick, N.L. Photodynamic therapy with the phthalocyanine photosensitizer Pc 4: the case experience with preclinical mechanistic and early clinical-translational studies Toxicol Appl Pharmacol. 2007 Nov 1;224(3):290-9 PMCID: PMC2128784
  4. Iyengar, S.K.Elston, R.C. The genetic basis of complex traits: rare variants or "common gene, common disease"? Methods Mol Biol. 2007;376:71-84
  5. Thompson, C.L., Klein, B.E., Klein, R., Xu, Z., Capriotti, J., Joshi, T., Leontiev, D., Lee, K.E., Elston, R.C.Iyengar, S.K.Complement factor H and hemicentin-1 in age-related macular degeneration and renal phenotypes Hum Mol Genet. 2007 Sep 1;16(17):2135-48
  6. Stein, C.M., Zalwango, S., Chiunda, A.B., Millard, C., Leontiev, D.V., Horvath, A.L., Cartier, K.C., Chervenak, K., Boom, W.H.,Elston, R.C., Mugerwa, R.D., Whalen, C.C., Iyengar, S.K. Linkage and association analysis of candidate genes for TB and TNFalpha cytokine expression: evidence for association with IFNGR1, IL-10, and TNF receptor 1 genes Hum Genet. 2007 Jul;121(6):663-73
  7. Nibbe, R.K., Markowitz, S., Myeroff, L., Ewing, R.Chance, M.R. Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol Cell Proteomics. 8(4):827-45. 2008. PMCID: PMC2667362
  8. Zhang, X., Guo, C., Chen, Y., Shulha, H.P., Schnetz, M.P., LaFramboise, T., Bartels, C.F., Markowitz, S., Weng, Z., Scacheri, P.C., Wang, Z. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nat Methods. 5(2):163-5. 2008 PMCID: PMC2435063.
  9. Zheng, X., Wintrode, P.L.Chance, M.R. Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin Structure. 2008 Jan;16(1):38-51
  10. Somani, A.K., Swick, A.R., Cooper, K.D.McCormick, T.S. Severe dermatomyositis triggered by interferon beta-1a therapy and associated with enhanced type I interferon signaling Arch Dermatol. 2008 Oct;144(10):1341-9
  11. Sugiyama, H., McCormick, T.S.Cooper, K.D., Korman, N.J. Alefacept in the treatment of psoriasis Clin Dermatol. 2008 Sep-Oct;26(5):503-8
  12. Toichi, E., Lu, K.Q., Swick, A.R., McCormick,T.S.Cooper, K.D. Skin-infiltrating monocytes/macrophages migrate to draining lymph nodes and produce IL-10 after contact sensitizer exposure to UV-irradiated skin J Invest Dermatol. 2008 Nov;128(11):2705-15
  13. Ke, M.S., Xue, L.Y., Feyes, D.K., Azizuddin, K., Baron, E.D., McCormick,T.S., Mukhtar, H., Panneerselvam, A., Schluchter, M.D., Cooper, K.D., Oleinick, N.L., Stevens, S.R. Apoptosis mechanisms related to the increased sensitivity of Jurkat T-cells vs A431 epidermoid cells to photodynamic therapy with the phthalocyanine Pc 4 Photochem Photobiol. 2008 Mar-Apr;84(2):407-14
  14. Stein, C.M., Zalwango, S., Malone, L.L., Won, S., Mayanja-Kizza, H., Mugerwa, R.D., Leontiev, D.V., Thompson, C.L., Cartier, K.C., Elston, R.C.Iyengar, S.K., Boom, W.H., Whalen, C.C. Genome scan of M. tuberculosis infection and disease in Ugandans PLoS One. 2008;3(12):e4094 PMCID: PMC2605555
  15. Arar, N.H., Freedman, B.I., Adler, S.G., Iyengar, S.K., Chew, E.Y., Davis, M.D., Satko, S.G., Bowden, D.W., Duggirala, R.,Elston, R.C., Guo, X., Hanson, R.L., Igo, R.P., Jr., Ipp, E., Kimmel, P.L., Knowler, W.C., Molineros, J., Nelson, R.G., Pahl, M.V., Quade, S.R., Rasooly, R.S., Rotter, J.I., Saad, M.F., Scavini, M., Schelling, J.R., Sedor, J.R., Shah, V.O., Zager, P.G., Abboud, H.E., Family Investigation of Nephropathy and Diabetes Research Group .Heritability of the severity of diabetic retinopathy: the FIND-Eye study. Invest Ophthalmol Vis Sci. 2008 Sep;49(9):3839-45 PMCID: PMC2583147
  16. Zhang, X., Guo, C., Chen, Y., Shulha, H.P., Schnetz, M.P., LaFramboise, T., Bartels, C.F., Markowitz, S., Weng, Z., Scacheri, P.C.Wang, Z. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies Nat Methods. 2008 Feb;5(2):163-5 PMCID: PMC2435063
  17. Lu, T., Jackson, M.W., Wang, B., Yang, M., Chance, M.R., Miyagi, M., Gudkov, A.V., Stark, G.R. Regulation of NF-kappaB by NSD1/FBXL11-dependent reversible lysine methylation of p65. Proc Natl Acad Sci U S A. 107(1):46-51. 2009. PMCID: PMC2806709
  18. Chance, M.R., Chang, J.S., Schlatzer, D.M., Miyagi, M. "Quantitative Proteomics" in Encyclopedia of Analytical Chemistry, R.A. Meyers, Ed., Wiley Publishing, p. 1-19, 2009.
  19. Schlatzer, D.M., Dazard, J.E., Dharsee, M., Ewing, R.M., Ilchenko, S., Stewart, I., Christ, G., Chance, M.R. Urinary protein profiles in a rat model for diabetic complications. Mol Cell Proteomics. 8(9):2145-58. 2009. PMCID: PMC2742441
  20. Chak, A., Falk, G., Grady, W.M., Kinnard, M., Elston, R., Mittal, S., King, J.F., Willis, J.E., Kondru, A., Brock, W., Barnholtz-Sloan, J. Assessment of familiality, obesity, and other risk factors for early age of cancer diagnosis in adenocarcinomas of the esophagus and gastroesophageal junction Am J Gastroenterol. 2009 Aug;104(8):1913-21 PMCID: PMC2864226
  21. Goodman, W.A., Levine, A.D., Massari, J.V., Sugiyama, H., McCormick,T.S.Cooper, K.D. IL-6 signaling in psoriasis prevents immune suppression by regulatory T cells J Immunol. 2009 Sep 1;183(5):3170-6 PMCID: PMC2903207
  22. Karnik, P., Tekeste, Z., McCormick,T.S., Gilliam, A.C., Price, V.H., Cooper, K.D., Mirmirani, P. Hair follicle stem cell-specific PPARgamma deletion causes scarring alopecia J Invest Dermatol. 2009 May;129(5):1243-57
  23. Jun, G., Guo, H., Klein, B.E., Klein, R., Wang, J.J., Mitchell, P., Miao, H., Lee, K.E., Joshi, T., Buck, M., Chugha, P., Bardenstein, D., Klein, A.P., Bailey-Wilson, J.E., Gong, X., Spector, T.D., Andrew, T., Hammond, C.J., Elston, R.C.Iyengar, S.K., Wang, B. EPHA2 is associated with age-related cortical cataract in mice and humans PLoS Genet. 2009 Jul;5(7):e1000584 PMCID: PMC2712078
  24. Erten, S., Li, X., Bebek, G., Li, J.Koyutürk, M. Phylogenetic analysis of modularity in protein interaction networks BMC Bioinformatics. 2009 Oct 14;10:333
  25. Schnetz, M.P., Bartels, C.F., Shastri, K., Balasubramanian, D., Zentner, G.E., Balaji, R., Zhang, X., Song, L., Wang, Z.,LaFramboise, T., Crawford, G.E., Scacheri, P.C. Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns Genome Res. 2009 Apr;19(4):590-601 PMCID: PMC2665778
  26. Yavas, G., Koyutürk, M., Ozsoyoğlu, M., Gould, M.P., LaFramboise, T. An optimization framework for unsupervised identification of rare copy number variation from SNP array data. Genome Biol. 10(10):R119. 2009. PMCID: PMC2784334
  27. Yavas, G., Koyutürk, M., Ozsoyoğlu, M., Gould, M.P., LaFramboise, T. Cokgen: a software for the identification of rare copy number variation from SNP microarrays. Pac Symp Biocomput. 2010: 371-82.
  28. Sun, X., Elston, R.Barnholtz-Sloan, J., Falk, G., Grady, W.M., Kinnard, M., Mittal, S.K., Willis, J.E., Markowitz, S., Brock, W., Chak, A. A segregation analysis of Barrett's esophagus and associated adenocarcinomas. Cancer Epidemiol Biomarkers Prev. 19(3):666-74, 2010. PMCID: PMC2838211
  29. Orban, T., Bereta, G., Miyagi, M., Wang, B., Chance, M.R., Sousa, M.C., Palczewski, K. Conformational changes in guanylate cyclase-activating protein 1 induced by Ca2+ and N-terminal fatty acid acylation. Structure. 18(1):116-26. 2010. PMCID: PMC2822722.
  30. Nibbe, R.K., Koyutürk, M.Chance, M.R. An integrative -omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol. 6(1):e1000639. 2010. PMCID: PMC2797084
  31. Kim, S., Abboud, H.E., Pahl, M.V., Tayek, J., Snyder, S., Tamkin, J., Alcorn, H., Jr., Ipp, E., Nast, C.C., Elston, R.C.Iyengar, S.K., Adler, S.G. Examination of association with candidate genes for diabetic nephropathy in a Mexican American population Clin J Am Soc Nephrol. 2010 Jun;5(6):1072-8 PMCID: PMC2879299
  32. Stein, C.M., Lu, Q., Elston, R.C., Freebairn, L.A., Hansen, A.J., Shriberg, L.D., Taylor, H.G., Lewis, B.A., Iyengar, S.K.Heritability Estimation for Speech-Sound Traits with Developmental Trajectories Behav Genet. 2010 Jul 10 [Epub ahead of print]
  33. Schnetz, M.P., Handoko, L., Akhtar-Zaidi, B., Bartels, C.F., Pereira, C.F., Fisher, A.G., Adams, D.J., Flicek, P., Crawford, G.E.,LaFramboise, T., Tesar, P., Wei, C.L., Scacheri, P.C. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression PLoS Genet. 2010 Jul 15;6(7):e1001023 PMCID: PMC2904778
  34. Gupta, S., Ghosh, S.K., Scott, M.E., Bainbridge, B., Jiang, B., Lamont, R.J., McCormick,T.S.Weinberg, A. Fusobacterium nucleatum-associated beta-defensin inducer (FAD-I): identification, isolation, and functional evaluation J Biol Chem. 2010 Nov 19;285(47):36523-31
  35. Zentner, G.E., Hurd, E.A., Schnetz, M.P., Handoko, L., Wang, C., Wang, Z., Wei, C., Tesar, P.J., Hatzoglou, M., Martin, D.M.,Scacheri, P.C. CHD7 functions in the nucleolus as a positive regulator of ribosomal RNA biogenesis Hum Mol Genet. 2010 Sep 15;19(18):3491-501
  36. Chowdhury, S.A., Nibbe, R.K., Chance, M.R.Koyutürk, M. .Subnet State Functions Define Dysregulated Subnetworks in Cancer,. B. Berger (Ed.): Proc. 14th Int.l Conf. Research in Computational Molecular Biology (RECOMB 2010), Springer LNCS 6044, pp. 80.95, 2010.
  37. Nibbe, R.K., Chowdhury, S.A., Koyuturk, M.Ewing, R.Chance, M.R. Protein-protein interaction networks and subnetworks in the biology of disease, WIRES: Systems Biology and Medicine, 3(3):357-67, 2011.
  38. Liu, Y., Patel, S.R., Nibbe, R.K., Maxwell, S., Chowdhury, S.A., Koyuturk, M., Zhu, X., Larkin, E.K., Buxbaum, S., Punjabi, N.M., Gharib, S., Redline, S., Chance, M.R. .Systems biology analyses of gene expression and genome wide association study data in obstructive sleep apnea., Pacific Symposium on Biocomputing 2011, 2011:14-25.
  39. Bebek, G., Koyutürk, M.Chance, M.R., Price, N.D. .INTEGRATIVE -OMICS FOR TRANSLATIONAL SCIENCE - Session Introduction., Pac Symp Biocomput.1-3, 2011
  40. Chowdhury, S.A., Nibbe, R.K., Chance, M.R.Koyuturk, M. CRANE: A method to define dysregulated subnetworks in cancer, Journal of Computational Biology, 18(3): 263-281, 2011. PMCID: PMC3123978
  41. Yang, J., Huang, J., Dasgupta, M., Sears, N., Miyagi, M., Wang, B., Chance, M.R., Chen, X., Du, Y., Wang, Y., Wang, Q., Lu, T., Zhang, X., Wang, Z., Stark, G.R. .Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes., Proc. Natl. Acad. Sci. U S A, 107(50):21499-504, 2010. PMCID: PMC3003019
  42. Barnholtz-Sloan, J.S.Chance, M.R. "Frontiers of oncology: biobanking resources for the 21st century" (invited editorial), Journal of Clinical Bioinformatics, 1:13, 2011.
  43. Yohannes, E., Ghosh, S.K., Jiang, B., McCormick, T.S.Weinberg, A., Hill, E., Faddoul, F., Chance, M.R., "Proteomics Signatures of Human Oral Epithelial Cells in HIV-infected Subjects." PloS One, submitted.
  44. Du Z, Song J, Wang Y, Zhao Y, Guda K, Yang S, Kao HY, Xu Y, Willis J, Markowitz SD, Sedwick D, Ewing RMWang Z. DNMT1 stability is regulated by proteins coordinating deubiquitination and acetylation-driven ubiquitination, Sci Signal. 3(146):ra80, 2010. PMCID: PMC3116231
  45. Erten S, Bebek G, Ewing RMKoyut�rk M. DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization, BioData Min. 4:19, 2011. PMCID: PMC3143097
  46. Miyagi M, Wan Q, Ahmad MF, Gokulrangan G, Tomechko SE, Bennett B, Dealwis C Histidine hydrogen-deuterium exchange mass spectrometry for probing the microenvironment of histidine residues in dihydrofolate reductase. PLoS One. 6(2):e17055, 2011. PMCID: PMC3040192